MicroLabVR: A VR-Based Platform for Interactive 3D Microbiome Data Visualization

Open Access

Issue		BIO Web Conf. Volume 195, 2025 2025 9^th International Conference on Biomedical Engineering and Bioinformatics (ICBEB 2025)


Article Number		02002
Number of page(s)		10
Section		Biomedical Imaging, Modeling and Visualization Technologies
DOI		https://doi.org/10.1051/bioconf/202519502002
Published online		14 November 2025

P.J. Sansonetti, War and peace at mucosal surfaces, Nature Reviews Immunology 4, 953–964 (2004). 10.1038/nri1499 [Google Scholar]
J.L. Foo, H. Ling, Y.S. Lee, M.W. Chang, Microbiome engineering: Current applica-tions and its future, Biotechnology Journal 12 (2017). 10.1002/biot.201600099 [Google Scholar]
J.C. Wooley, A. Godzik, I. Friedberg, A primer on metagenomics, PLoS Computational Biology 6, e1000667 (2010). 10.1371/journal.pcbi.1000667 [Google Scholar]
L. Zhang, F. Chen, Z. Zeng, M. Xu, F. Sun, L. Yang, X. Bi, Y. Lin, Y. Gao, H. Hao et al., Advances in metagenomics and its application in environmental microorganisms, Frontiers in Microbiology 12 (2021). 10.3389/fmicb.2021.766364 [Google Scholar]
M.A. Moran, B. Satinsky, S.M. Gifford, H. Luo, A. Rivers, L.K. Chan, J. Meng, B.P. Durham, C. Shen, V.A. Varaljay et al., Sizing up metatranscriptomics, The ISME Jour-nal 7, 237–243 (2012). 10.1038/ismej.2012.94 [Google Scholar]
T. Ojala, E. Kankuri, M. Kankainen, Understanding human health through metatranscriptomics, Trends in Molecular Medicine 29, 376–389 (2023). 10.1016/j.molmed.2023.02.002 [Google Scholar]
S. Mirete, V. Morgante, J.E. González-Pastor, Functional metagenomics of ex-treme environments, Current Opinion in Biotechnology 38, 143–149 (2016). 10.1016/j.copbio.2016.01.017 [Google Scholar]
Y. Wang, Y. Zhou, X. Xiao, J. Zheng, H. Zhou, Metaproteomics: A strategy to study the taxonomy and functionality of the gut microbiota, Journal of Proteomics 219, 103737 (2020). 10.1016/j.jprot.2020.103737 [Google Scholar]
M. Kumar, B. Ji, K. Zengler, J. Nielsen, Modelling approaches for studying the micro-biome, Nature Microbiology 4, 1253–1267 (2019). 10.1038/s41564-019-0491-9 [Google Scholar]
X. Liu, J.W. Locasale, Metabolomics: A primer, Trends in Biochemical Sciences 42, 274–284 (2017). 10.1016/j.tibs.2017.01.004 [Google Scholar]
M. Banwarth-Kuhn, S. Sindi, How and why to build a mathematical model: A case study using prion aggregation, Journal of Biological Chemistry 295, 5022–5035 (2020). 10.1074/jbc.rev119.009851 [Google Scholar]
E.H. Wintermute, P.A. Silver, Emergent cooperation in microbial metabolism, Molecu-lar Systems Biology 6 (2010). 10.1038/msb.2010.66 [Google Scholar]
E. Bauer, J. Zimmermann, F. Baldini, I. Thiele, C. Kaleta, Bacarena: Individual-based metabolic modeling of heterogeneous microbes in complex communities, PLOS Com-putational Biology 13, e1005544 (2017). 10.1371/journal.pcbi.1005544 [Google Scholar]
M.A. Henson, T.J. Hanly, Dynamic flux balance analysis for synthetic microbial com-munities, IET Systems Biology 8, 214–229 (2014). 10.1049/iet-syb.2013.0021 [Google Scholar]
J.D. Orth, I. Thiele, B.Ø. Palsson, What is flux balance analysis?, Nature Biotechnology 28, 245–248 (2010). 10.1038/nbt.1614 [Google Scholar]
K. Raman, N. Chandra, Flux balance analysis of biological systems: applications and challenges, Briefings in Bioinformatics 10, 435–449 (2009). 10.1093/bib/bbp011 [Google Scholar]
K.J. Kauffman, P. Prakash, J.S. Edwards, Advances in flux balance analysis, Current Opinion in Biotechnology 14, 491–496 (2003). 10.1016/j.copbio.2003.08.001 [Google Scholar]
W. Harcombe, W. Riehl, I. Dukovski, B. Granger, A. Betts, A. Lang, G. Bonilla, A. Kar, N. Leiby, P. Mehta et al., Metabolic resource allocation in individual microbes deter-mines ecosystem interactions and spatial dynamics, Cell Reports 7, 1104–1115 (2014). 10.1016/j.celrep.2014.03.070 [Google Scholar]
B. Borer, D. Or, Spatiotemporal metabolic modeling of bacterial life in complex habitats, Current Opinion in Biotechnology 67, 65–71 (2021). 10.1016/j.copbio.2021.01.004 [Google Scholar]
J.H. Holland, Complex adaptive systems, Daedalus 121, 17 (1992). [Google Scholar]
V. Grimm, E. Revilla, U. Berger, F. Jeltsch, W.M. Mooij, S.F. Railsback, H.H. Thulke, J. Weiner, T. Wiegand, D.L. DeAngelis, Pattern-oriented modeling of agent-based complex systems: Lessons from ecology, Science 310, 987–991 (2005). 10.1126/sci-ence.1116681 [Google Scholar]
H. Kaul, Y. Ventikos, Investigating biocomplexity through the agent-based paradigm, Briefings in Bioinformatics 16, 137–152 (2013). 10.1093/bib/bbt077 [Google Scholar]
G. An, Q. Mi, J. Dutta-Moscato, Y. Vodovotz, Agent-based models in transla-tional systems biology, WIREs Systems Biology and Medicine 1, 159–171 (2009). 10.1002/wsbm.45 [Google Scholar]
T. Shashkova, A. Popenko, A. Tyakht, K. Peskov, Y. Kosinsky, L. Bogolubsky, A. Raig-orodskii, D. Ischenko, D. Alexeev, V. Govorun, Agent based modeling of human gut microbiome interactions and perturbations, PLOS ONE 11, e0148386 (2016). 10.1371/journal.pone.0148386 [Google Scholar]
S. Pirch, F. Müller, E. Iofinova, J. Pazmandi, C.V.R. Hütter, M. Chiettini, C. Sin, K. Boz-tug, I. Podkosova, H. Kaufmann et al., The vrnetzer platform enables interactive net-work analysis in virtual reality, Nature Communications 12 (2021). 10.1038/s41467-021-22570-w [Google Scholar]
M.B. Biggs, J.A. Papin, Novel multiscale modeling tool applied to pseudomonas aerug-inosa biofilm formation, PLoS ONE 8, e78011 (2013). 10.1371/journal.pone.0078011 [Google Scholar]
G. Wilson, D.A. Aruliah, C.T. Brown, N.P. Chue Hong, M. Davis, R.T. Guy, S.H.D. Haddock, K.D. Huff, I.M. Mitchell, M.D. Plumbley et al., Best practices for scientific computing, PLoS Biology 12, e1001745 (2014). 10.1371/journal.pbio.1001745 [Google Scholar]
S. Mangul, T. Mosqueiro, R.J. Abdill, D. Duong, K. Mitchell, V. Sarwal, B. Hill, J. Brito, R.J. Littman, B. Statz et al., Challenges and recommendations to improve the installability and archival stability of omics computational tools, PLOS Biology 17, e3000333 (2019). 10.1371/journal.pbio.3000333 [Google Scholar]
L. Barone, J. Williams, D. Micklos, Unmet needs for analyzing biological big data: A survey of 704 nsf principal investigators, PLOS Computational Biology 13, e1005755 (2017). 10.1371/journal.pcbi.1005755 [Google Scholar]
J. Zheng, K. Chan, I. Gibson, Virtual reality, IEEE Potentials 17, 20–23 (1998). 10.1109/45.666641 [Google Scholar]
C. Jennett, A.L. Cox, P. Cairns, S. Dhoparee, A. Epps, T. Tijs, A. Walton, Measuring and defining the experience of immersion in games, International Journal of Human-Computer Studies 66, 641–661 (2008). 10.1016/j.ijhcs.2008.04.004 [CrossRef] [Google Scholar]
C. Donalek, S.G. Djorgovski, A. Cioc, A. Wang, J. Zhang, E. Lawler, S. Yeh, A. Maha-bal, M. Graham, A. Drake et al., Immersive and collaborative data visualization using virtual reality platforms, in 2014 IEEE International Conference on Big Data (Big Data) (IEEE, 2014), http://dx.doi.org/10.1109/BigData.2014.7004282 [Google Scholar]
J.H. Moore, R.C.S. Lari, D. Hill, P.L. Hibberd, J.C. Madan, Human microbiome visualization using 3d technology (World Scientific, 2010), p. 154–164, ISBN 9789814335058, http://dx.doi.org/10.1142/9789814335058_0017 [Google Scholar]
M. Aichem, K. Klein, T. Czauderna, D. Garkov, J. Zhao, J. Li, F. Schreiber, Towards a hybrid user interface for the visual exploration of large biomolecular networks using virtual reality, Journal of Integrative Bioinformatics 19 (2022). 10.1515/jib-2022-0034 [Google Scholar]
U. Technologies, Unity (2024), https://unity.com/de [Google Scholar]
Meta, Tech. rep., Meta (2024), https://developers.meta.com/horizon/resources/compare-devices/ [Google Scholar]
Blender Foundation, Blender – Open Source 3D Creation Suite, https://www.blender.org/ (2025), last accessed: 10 April 2025 [Google Scholar]
M.B.I. Palash, M.F. Islam, F. Ahamed, Mitigating cybersickness in virtual reality: Chal-lenges and solutions, International Journal of Novel Research in Computer Science and Software Engineering 12, 12 (2025). 10.5281/zenodo.14608484 [Google Scholar]
Android Developers, Storage Access Framework, https://developer.android.com/guide/topics/providers/document-provider (2025), last accessed: 19 April 2025 [Google Scholar]
gkngkc, UnityStandaloneFileBrowser GitHub Repository, https://github.com/gkngkc/UnityStandaloneFileBrowser/tree/master?tab=readme-ov-file (2025), last accessed: 19 April 2025 [Google Scholar]

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